ebgu/rodenttracker

An open-source tracking toolkit for EPM of OFT assay of mice or rats.

RodentTracker

An open-source tracking toolkit for EPM of OFT assay of mice or rats.

This script could NOT run on WINDOWS !!!

If you indeed need to run it on Windows, please modify this code following this instruction. We would fix it in the next version.

To create conda environment:

conda env create -f RodentTracker.yml 

This toolkit includes three major part.

First, it converts videos into sequential images for downstream processings. It would also correct images based on four key points you choose.

Second, it would remove the background of each image. You can either choose the background to be the average frame of the video, or the average frame of the first ten seconds of the video. It is not neccessary if you have a clean background.

Finally, it could track the centroid of the animal.

Scripts to process generated logs are also provide.

Enjoy!

Best, Yinjun

rodenttracker's Issues

Problem in data preprocessing

Hi Yinjun,

Your work on self-supervised features extraction is amazing! However, here is still a few problems when I try to set Selfee up on a online platform (as RTX3090 is still not that accessible for our traditional biology lab).

The first problem is in the "data preprocessing" step. I tried to use your rodenttracker to extract frames and remove background. I modified the Supertracker_OFT_Template script as suggested (I don't know if I have modified the correct script):

When running it in terminal, it returns a error like this:

error: OpenCV(4.1.2) /io/opencv/modules/imgproc/src/color.cpp:182: error: (-215:Assertion failed) !_src.empty() in function 'cvtColor'

I search the internet for it and find some say it is because the path is relative path but not absolute path. But there seems to be no relative path pass to any functions. Could you please give some more detailed instructions to me on this problem? Many thanks! Hoping to hear from you soon.